Created a debug output mode that dumps the the exact inputs/outputs of the PairHMM to a file #7660
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@droazen could you take a look at this branch? |
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@jamesemery Back to you with a couple of quick comments. Main question is why the AVX_LOGLESS_CACHING test case is disabled
...adinstitute/hellbender/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java
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...adinstitute/hellbender/tools/walkers/haplotypecaller/LikelihoodEngineArgumentCollection.java
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...adinstitute/hellbender/tools/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
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src/main/java/org/broadinstitute/hellbender/utils/pairhmm/PairHMM.java
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| if(doProfiling) | ||
| logger.info("Total compute time in PairHMM computeLogLikelihoods() : "+(pairHMMComputeTime*1e-9)); | ||
| if(doProfiling) { | ||
| logger.info("Total compute time in PairHMM computeLogLikelihoods() : " + (pairHMMComputeTime * 1e-9)); |
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What's the time unit here? Seconds?
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seconds I believe just as it has in the past for gatk. Its using nanoTime so converting to seconds should be 10^-9.
| */ | ||
| @Advanced | ||
| @Hidden | ||
| @Argument(fullName="pair-hmm-results-file", doc="File to write exact pairHMM inputs/outputs to for debugging purposes", optional = true) |
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Do all of the available HMMs respect this argument, or only some of them? If only some, list the ones that respect it.
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all of them as far as i've tested. I have a test for all of them but the AVX was producing some different output on travis...
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| if (debugOutputStream!= null) { | ||
| try { | ||
| debugOutputStream.write("\n" + new String(alleleBases) + " " + new String(readBases) + " " + SAMUtils.phredToFastq(readQuals) + " " + SAMUtils.phredToFastq(readInsQuals) + " " + SAMUtils.phredToFastq(readDelQuals) + " " + SAMUtils.phredToFastq(overallGCP) + " " + String.format("%e",lk)); |
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Confirming that the values in this table will never contain internal whitespace?
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I don't think so. If the alleles or the phred to fastq mehtods are returning results with whitespaces in them we have much bigger problems...
| @DataProvider(name="PairHMMResultsModes") | ||
| public Object[][] PairHMMResultsModes() { | ||
| return new Object[][] { | ||
| //{PairHMM.Implementation.AVX_LOGLESS_CACHING, new File(TEST_FILES_DIR, "expected.AVX.hmmresults.txt")}, //TODO disabled because of failures on travis |
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Can you elaborate on why this is disabled? Ideally we want test coverage for the default HMM in GATK...
…ts of of the HMM to a file for debugging purposes
jamesemery
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@droazen I loosened the failing test and responded to your comments? Anything else before we can get this in? |
Resolves #7647